Welcome to the Rafiki home page,where fun and learning go hand in hand.

Home of Code World,

and exploring the genetic code.

Happy Day!

Dr. Rafiki is writing again.

I had completely given up on this whole thing. It was taking up too much time and too many resources, and returning very little.

If you peruse this site, keep in mind that every web page, device, picture, description and virtually every idea was generated by one person. And this reflects just a tiny fraction of those efforts. Then realize that this person has a life, a job, a serious golf addiction, four kids, a wife, and four cats.

What changed?

I decided to sell Mutation, the kid sister of Code World that is not mentioned anywhere here because of intellectual property concerns.

The great state of Indiana somehow decided that Rafiki Inc. wasn’t worthy of being called a business. So, I guess, now it is not.

Dr. Rafiki then started another business which is cleverly called White Golf LLC. The website for that is HERE

When I set out to sell Mutation, I made the decision to not mention the genetic code. It’s too much trouble, and the idea seems to repel people. I was going to just sell it as a toy, since it’s such a cool toy.

Then I was in a waiting period to begin selling, and I’ll be damned if it didn’t happen again. How do you sell somebody a toy and not tell them it is the first life form on earth and the single best clue to the origin of life?

So once again, I set out to find a way to explain this.

This whole collection of activity and ideas started with a single, simple idea: Code World is the genetic code, and life is playing Code World.

In a single instant, I knew this was true, I understood it, I knew what it meant. Because of that, I thought everybody else could do the same. All I would need do was show it to people and it would have the exact same effect.

Boy was I ever wrong about that.

There are lots of problems with this notion. Perhaps the biggest problem was that I failed to understand just exactly how it was that I knew all this in the first place, and why I understood it, and why it had such great meaning.

Also, people seem to think this is a small idea with few consequences. That’s a laugh. I can’t imagine a bigger idea with more consequences than this one. We need not go into that here.

So I started writing again. I actually began by starting a novel. I always wanted to write a novel. Then I needed help with the novel. I needed somebody to invent a new branch of mathematics for me, and so I did what I could to describe that branch of mathematics and how I would use it in the novel. Then I wrote a piece to describe why that branch of mathematics was needed and where it would fit into the larger picture. Then people, once again, said they couldn’t understand a word of it, and I needed to dum it down. So I basically wrote the second piece again, and hopefully made it dum enough.

These three pieces represent about 80,000 words, to go along with the million or so words I’d already written. Now I realize that these new pieces merely describe what Code World is; they don’t explain what it means. To me, that is perhaps the most important part, so I finally wrote that one too..

Ironically, the one thing I haven’t finished is the novel, and I probably won’t. Who’d ever read that?

These pieces are presented here in reverse order. They are merely first drafts, and that’s probably all they will ever be. Quite a bit of redundancy can be expected. Quite a bit of insanity can be expected. I happily acknowledge that I am totally insane. That’s exactly what it takes to do anything like this. But I’m also totally sure that all of this stuff is totally right.

I am going to start selling some toys and see how it goes. I am putting this out there in this form because I can’t think of any other way to do it. I’ve tried everything I can think of and nothing seems to work.

I guess I’m not really giving up, even though I said I was. It’s just too important, and it is fun… in a sad sort of way.

This is the best way to explain it: Code World is the genetic code, and life is playing Code World.

If that’s not important to you, I can surely understand that. Half the adult population thinks Natural Selection is a scientific hoax, and the earth is only 6,000 years old. I can understand why they would be naturally repelled by the idea that a toy has something to do with the logical formation of life on earth.

I’m going to leave the rest of this website pretty much the way it is because I don’t have time to mess with it, and it’s not hurting anybody. It is a living museum of the various ways I have tried to explain this whole thing. The ideas are still good, useful, and entertaining. It’s a gold mine if you are looking for ideas in this area. You just need to take a lot of it with a grain of salt.

July 19, 2014

Old stuff:

The Perfect Code Theory

The Perfect Code Theory is a name I have given to a collection of ideas about
molecular information to contrast them with the ideas that make up the conventional
theory about the genetic code and its role in protein formation. The central
premise of my theory is that a perfect code of spatial logic exists in the
universe. The co-dependent processes of DNA and protein formation are consequences
of that logic. Conversely, the narrow relationship between codons and amino
acids - at first called the genetic code - reflects but a tiny portion of that
logic. A proper understanding of protein formation will now require a complete
rejection of the conventional theory. Furthermore, an enlightened view of the
fundamental logic driving life on earth will require a proper understanding
of the relationship between nucleotides and protein as it manifests a real
molecular system of information based on a perfect code of spatial logic.

To be honest, articulation of my theory to date has mostly consisted of simply
complaining that the old theory is completely wrong. I have a number of good
reasons to believe this, but it has proven insufficient to merely call for
the outright rejection of a universally accepted theory. So, I am now offering
The Perfect Code Theory as a positive alternative rather than merely a negation
of the universally accepted theory. I will put forth a number of hypotheses,
arguments, explanations and proofs to support my general theory, and I will
compare and contrast the implications of these with those of the conventional
theory. Ultimately one must decide whether to keep or reject the conventional
theory since it is mutually exclusive with the Perfect Code Theory.

A quick understanding of my theory can be gained by way of analogy with ordinary
table salt, which is a sodium chloride crystal. There exists a perfect code
of spatial logic in the universe that guides the formation of table salt. This
logic can be completely described by a cube. Formation of the crystal is achieved
by individual atoms of sodium and chloride organizing themselves according
to the logic demonstrated by the vertices of dual tetrahedrons that form a
cube. The “plan” for table salt is to make cubes from sodium tetrahedrons
dual to chloride tetrahedrons. The only molecular machinery required is the
molecular cube itself. The molecular information it generates and stores is
trivial. In comparison, the Perfect Code Theory holds that a similar “plan” exists
for protein and DNA. It is based not on a single form but on logical relationships
between forms. The spatial logic is only slightly more complex, but the molecular
manifestation of that logic is indeed profoundly complex, and the machinery
required to translate the molecular information it generates encompasses a
good part of known biochemistry. Life represents the function of time-dependent
creation and accumulation of molecular information in this system of spatial
logic. The general concept is deceptively simple, but the task of describing
its actual operation will surely challenge the limits of human cognition.

The reason that I have chosen the name ‘the Perfect Code Theory’ is
because it puts my theory in stark opposition to the conventional theory. It
is currently an accepted idea that no spatial information is stored in DNA
and translated into protein. This idea exists in numerous word forms, but it
can be communicated by saying that the genetic code is one-dimensional. This
means that the relationship between codons and amino acids exists only to translate
sequences of nucleotides into sequences of amino acids. The one dimension of
molecular information stored in DNA and translated into protein is manifest
by a sequence of amino acids found in every protein. If this were true then
no code of spatial logic – perfect or otherwise – is ever required
to generate this system in nature or to describe this molecular system amongst
man. However, this central idea has never actually been tested or empirically
demonstrated to be true. In fact it is logically unappealing, conceptually
devastating, and it has proven time and again to be empirically false. Therefore,
only when we systematically explore the ramifications of the Perfect Code Theory
will we finally realize the epistemic devastation that is wrought by the false
central premise of the conventional theory. The contrast cannot be more stark:
either protein formation is based on spatial logic or it is completely devoid
of it. The choice is clear; the choice has been made, and the choice that was
made is clearly wrong. It is time to consider alternative theories, and that
is precisely what I am doing here.

Older stuff::

This website is a collection of fanciful ramblings about
symmetry and the genetic code. We hope you enjoy it. There is a lot of material
here, and perhaps it strays a bit more than it should, so to cut
to the chase here are some stunning conclusions about the genetic
code.

The best way to view the genetic code and all of the relationships between
its component parts is on the surface of a sphere.

For protein translation, the axiom "primary sequence determines tertiary
structure" is false. A single primary sequence can and does fold into more
than one
tertiary
structure under physiologic conditions.

The genetic code can and does translate more molecular information from
mRNA to protein than just primary sequence.

A complete understanding of the genetic code must include the role played
by tRNA during protein translation. Different sets of tRNA will yield
different translations of molecular information.

The genetic code has an overall symmetry that represents the primary
organizing force behind the code itself. The genetic code is not only an
operating system that builds proteins but also a search engine that efficiently
finds
proteins
and protein populations. The symmetry of genomes and the symmetry of their
codes of translation are tightly integrated.

Although seemingly heretical, these statements are all logically
true or have been experimentally proven true. Anyone who would like to dispute
any
of these
claims
should contact me at the above link, and I will post your argument and your
evidence here.

It appears that life is doing math with molecules. There is a striking similarity
to life on earth and the history of mathematics, where the development of our
complex and various branches of mathematics parallel that of a living system
of molecules interacting to exchange molecular information. Unfortunately,
our accepted model of this system is flawed and entirely inadequate. We have
no formal system for defining key components of the system and therefore have
no hope
of understanding the relationships between these components. The language and
icons that we currently use are wholly inadequate. Therefore, all of biology
will benefit by adopting the basic tools and techniques used for centuries
by mathematicians
to build a logical and coherent system of thought and communication. I believe
that set theory will provide a foundation of logic and the essential tools
for defining key components of biological systems and the informative relationships
between them. I believe that symmetry and groups will be a key component of
quantifying molecular information and achieving a better understanding of its
translation.